The aim of this study was to characterize, using metagenomic shotgun DNA sequencing, the intrauterine microbial population and its predicted functional diversity within healthy cows and cows presenting purulent vaginal discharge (PVD). Twenty Holstein dairy cows from a single farm were enrolled in the study at 25 to 35 d postpartum. Purulent vaginal discharge was diagnosed by retrieving and scoring vaginal discharge using the Metricheck device (Simcro, Hamilton, New Zealand). Intrauterine samples for metagenomic analysis were collected by the cytobrush technique from 8 cows diagnosed with PVD and 12 healthy cows. Pair-end sequencing was performed using the Illumina MiSeq platform (Illumina Inc., San Diego, CA). Metagenomic sequences were analyzed using the MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/), and the STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) was used to study statistically significant differential abundance of taxonomic and functional features between the 2 metagenomes. Additionally, the total number of bacterial 16S rDNA copies was estimated by real-time PCR. Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum in the uterine microbiota from cows with PVD, and Fusobacteria was almost completely absent in the healthy uterine microbiota. Moreover, species belonging to the genus Trueperella were present only in the uterine microbiota of PVD cows. The increased abundance of Fusobacteria and the unique presence of Trueperella in the PVD cows highlight the important role of these bacteria in the pathogenesis of PVD. Genes encoding cytolethal distending toxin were exclusive to the microbiota of PVD cows. Similarly, genes associated with lipid A modification were present only in samples from PVD cows; such modification is associated with greater resistance to cationic antimicrobial peptides. Conversely, genes encoding bacteriocins and ribosomally antibacterial peptide were exclusively found in the healthy uterine microbiota and dominated by tolerance to colicin E2. No difference was observed in total bacterial load between the 2 microbiotas. This study provides deep insight into the uterine microbial community in health and disease. The observations that the healthy microbiota is tolerant to colicin E2, whereas the uterine microbiota of PVD cows produces cytolethal distending toxins and modifies its lipopolysaccharides suggest that species-intrinsic factors may be more relevant than bacterial abundance to the development of disease or maintenance of health in the dairy cow postpartum uterus.